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I recently had the head replaced on a 4.0 01 Wrangler due to the 0331 issues. Spark plugs were changed as well. However now the check engine light is coming on with longer distance travels. Does not flash, just illuminates. I pulled the codes and they are P0304, P0305, P0306, and P0300. The engine does not seem to misfire and I was traveling 70-75 without much issues. I have driven it around 300 miles since the head replacement. The light does not come on with shorter distance driving around town, only 1-2 hour drives. It was a brand new head from Clearwater as well. Any help would be greatly appreciated!
 

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I would not expect the head to be cause for misfire.
If you clear the code, do the cylinder-specific codes (P0305/05/06) come back to the same cylinders?

Usual suspects would be on the ignition side of things or related sensors.
Could very well be Crankshaft Position Sensor, Cam Position Sensor or distributor switch plate (if it has one). Mopar sensors would be the best choice.

Nobody likes "throwing parts" at a problem, but sometimes it is difficult to get a diagnosis down to a specific part when things are related to ignition misfire codes. If it were mine, I would start with the cheapest part first and see if that solves the problem. If not, move on to the next. Heck! These three items together are less than $300 combined. Maybe just get them all at once and be done with the codes...
 

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Discussion Starter #3
It has happened twice so far and yes those codes only. I do not think it is an ignition rail issue due to reading there are basically 3 feeding due cylinders each, and cylinder 3 has not misfired as of yet. I will look into the other sensors you have stated!
 

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I agree it does not sound like ignition.

Are you getting a high idle or maybe were when you first got it running after the head replacement?

Since it is only the back 3 cylinders I would say it might be that you have a vacuum leak from the back half of the intake manifold.

I think the brake booster & crankcase vent hoses both attach to the back half so would check there.

If both look good with the engine running at idle you can spray something like WD-40 around & along their length to see if you get a change in idle speed & if no idle speed change then do the same around the intake to head gasket area.
 
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